Genome-wide Scan of 29,141 African Americans Finds No Evidence of Directional Selection since Admixture

Gaurav Bhatia, Arti Tandon, Nick Patterson, Melinda C. Aldrich, Christine B. Ambrosone, Christopher Amos, Elisa V. Bandera, Sonja I. Berndt, Leslie Bernstein, William J. Blot, Cathryn H. Bock, Neil Caporaso, Graham Casey, Sandra L. Deming, W. Ryan Diver, Susan M. Gapstur, Elizabeth M. Gillanders, Curtis C. Harris, Brian E. Henderson, Sue A. Ingles, William Isaacs, Phillip L. De Jager, Esther M. John, Rick A. Kittles, Emma Larkin, Lorna H. McNeill, Robert C. Millikan, Adam Murphy, Christine Neslund-Dudas, Sarah Nyante, Michael F. Press, Jorge L. Rodriguez-Gil, Benjamin A. Rybicki, Ann G. Schwartz, Lisa B. Signorello, Margaret Spitz, Sara S. Strom, Margaret A. Tucker, John K. Wiencke, John S. Witte, Xifeng Wu, Yuko Yamamura, Krista A. Zanetti, Wei Zheng, Regina G. Ziegler, Stephen J. Chanock, Christopher A. Haiman, David Reich, Alkes L. Price

The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study's conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas.